Enforce pre-commit mypy type checking

### Context
We have a lot of type checking rules in the refine.bio code base. However, those checks aren't enforced by pre-commit config.

### Problem or idea
We should add the mypy hook and fix those ~500 errors upon pre-commit run

### Solution or next step
Do the tedious work, clean up the code.

Start by locating the pre-commit configuration and reviewing the repository's existing mypy settings. Enable the mypy hook, run pre-commit to identify the reported errors, and consider the work complete when the hook runs successfully without those errors.

Written by the indexing model from the issue text.